A Genome-Wide Analysis of the Chloroplast NADH Dehydrogenase-Like Genes in Zostera Marina

The chloroplast NADH dehydrogenase-like (NDH) complex, homologous to respiratory complex I, participates in photosystem I cyclic electron flow (PSI-CEF) and chlororespiration in photosynthesis. Phylogenetic analyses indicated that Zostera marina, a widely distributed seagrass, has a complete NDH complex, which is rarely observed in marine macrophytes. We identified all 31 ndh genes necessary for the functional NDH complex, of which ndhB and pnsb3 occurred as duplication events. Secondary structural analyses of antiporter-like subunits showed that the long amphipathic helix of NdhF was lost in Z. marina, which could exhibit an alternative mode in the generation of trans-thylakoid proton gradient. The splicing pattern of ndh exhibited tissue-specific patterns and responded to light stress. RNA editing in Z. marina presented the ancestral pattern with many of the primitive editing sites and types. The partial editing in ndhF reflected the link between light stress and RNA editing. Moreover, the predominant expression in leaves of most ndh genes suggested that their major function is in photosynthesis. The quantitative real time-PCR results show that the expression of ndh was significantly upregulated in response to light stress. Nevertheless, there were two diverse responsive mechanisms of the NDH complex in PSI-CEF and chlororespiration. Overall, the presence of a complete structure, upregulated gene expression level, and multiple post-transcriptional regulations could provide a molecular basis for the powerful NDH complex and enable Z. marina to maintain effective photosynthetic performance.